I kind of lean towards rewarding the #1 team for their regular season success. If a team plays a full conference schedule and ends the regular season as #1, why would you punish them for losing one game during a tournament that lasts a week.
Now, in Burns/Shelby's case this week, they both finished tied for 1st in the conference. Splitting the season series. I would assume, that which ever team goes further in the tournament, will get the one seed.
My junior year many moons ago, us and Kings Mountain tied for the 1 seed during the regular season. We both got upset in the semi-finals and had to play a tie breaker game to see who got the one seed. But if the rule of whoever wins the conference tournament gets a one seed were in effect, neither of us would have gotten it. It's like the NCAA, just because you win your conference tournament, doesn't guarantee you a high seed in the big dance, just guarantees you a spot.